Portable Blender (3D Suite)
For those of you who doesn't know, blender (current version 2.42) is a 3D computer graphic suite (like maya and 3dsmax). It is extremely small (only 6mb for a full installation) and is basically already 'portable', since it does not rely on any windows service, dll, or registry setting.
for more info: http://blender.org/cms/Home.2.0.html
Blender is, IMO, an ideal portable app, it is small, very 'portable' already, and is opensource so any modification is possible.